[DO NOT MERGE]#9045

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jamesemery wants to merge 37 commits intomasterfrom

je_updateCondaEnvironment

Commits on Nov 12, 2024

first attempt at a changed environment
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Commits on Nov 15, 2024

updating pytorch to newer version that carries some risk
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gore
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back to basics
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uncommenting some
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trying two more dependencies
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enabling two more
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Commits on Nov 18, 2024

was it cyvcf?
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mmninga?
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Commits on Nov 19, 2024

another minor alteration of python environment
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bioconda cyvcf2 is probably a conflict
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bioconda cyvcf2 is probably a conflict
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Commits on Dec 4, 2024

Reverting to 2.1.0
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Commits on Dec 9, 2024

trying to bundle the cuda installation via conda
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pairing up the correct cuda compatable pytroch version
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change the channel
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testing with only cuda backend?
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change the channel
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Commits on Dec 10, 2024

testing if the other mkl invocation was the problem
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testing if the other mkl invocation was the problem
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finally! python has lead us from gods light
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finally! python has lead us from gods light
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this should probably work
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Commits on Dec 19, 2024

put the code in the right place, now need to build a pythonscriptexecutor to run it and make sure it gets installed for running correctly
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Commits on Jan 10, 2025

hopefully what is needed for docker building proper
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did this really stop working?
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python installation is dizzying
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moving the cuda drivers into the right stage of the build
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Commits on Jan 13, 2025

names have power
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fixing a silly mistake
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Commits on Jan 15, 2025

made a somewhat robust mechanism for converting to the python argument outputs for permutect
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Commits on Jan 16, 2025

some more script editing
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some more script editing
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Commits on Jan 17, 2025

added the next few tasks from the main wdl
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added the next few tasks from the main wdl
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Commits on Jan 21, 2025

added docstore bindings to the permutect wdls
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maybe the branches are the problem
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